PDBsum entry: 2roc

Apoptosis

PDB id: 2roc

Contents

Protein chains

162 a.a. *

27 a.a. *

* Residue conservation analysis

PDB id:

2roc

Name:

Apoptosis

Title:

Solution structure of mcl-1 complexed with puma

Structure:

Induced myeloid leukemia cell differentiation protein mcl-1 homolog. Chain: a. Fragment: residues 152-308. Synonym: bcl-2-related protein eat/mcl1, mcl-1. Engineered: yes. Bcl-2-binding component 3. Chain: b. Fragment: bh3 domain, residues 130-155.

Source:

Mus musculus. Mouse. Gene: mcl-1. Expressed in: escherichia coli. Expression_system_variant: de3. Gene: puma.

NMR struc:

20 models

Authors:

C.L.Day,C.Smits,F.C.Fan,E.F.Lee,W.D.Fairlie,M.G.Hinds

Key ref:

C.L.Day et al. (2008). Structure of the BH3 domains from the p53-inducible BH3-only proteins Noxa and Puma in complex with Mcl-1. J Mol Biol, 380, 958-971. PubMed id: 18589438 DOI: 10.1016/j.jmb.2008.05.071

Date:

17-Mar-08 Release date: 08-Jul-08

Protein chain

P97287  (MCL1_MOUSE) -  Induced myeloid leukemia cell differentiation protein Mcl-1 homolog

Seq: 331 a.a.

Struc: 162 a.a.*

Protein chain

Q99ML1  (BBC3_MOUSE) -  Bcl-2-binding component 3

Seq: 193 a.a.

Struc: 27 a.a.*

* PDB and UniProt seqs differ at 6 residue positions (black crosses)

 Gene Ontology (GO) functional annotation 

• Biological process: regulation of apoptosis (1 term)

DOI no: 10.1016/j.jmb.2008.05.071

J Mol Biol 380:958-971 (2008)

PubMed id: 18589438

Structure of the BH3 domains from the p53-inducible BH3-only proteins Noxa and Puma in complex with Mcl-1.

C.L.Day, C.Smits, F.C.Fan, E.F.Lee, W.D.Fairlie, M.G.Hinds.

ABSTRACT

Pro-survival proteins in the B-cell lymphoma-2 (Bcl-2) family have a defined specificity profile for their cell death-inducing BH3-only antagonists. Solution structures of myeloid cell leukaemia-1 (Mcl-1) in complex with the BH3 domains from Noxa and Puma, two proteins regulated by the tumour suppressor p53, show that they bind as amphipathic alpha-helices in the same hydrophobic groove of Mcl-1, using conserved residues for binding. Thermodynamic parameters for the interaction of Noxa, Puma and the related BH3 domains of Bmf, Bim, Bid and Bak with Mcl-1 were determined by calorimetry. These unstructured BH3 domains bind Mcl-1 with affinities that span 3 orders of magnitude, and binding is an enthalpically driven and entropy-enthalpy-compensated process. Alanine scanning analysis of Noxa demonstrated that only a subset of residues is required for interaction with Mcl-1, and these residues are localised to a short highly conserved sequence motif that defines the BH3 domain. Chemical shift mapping of Mcl-1:BH3 complexes showed that Mcl-1 engages all BH3 ligands in a similar way and that, in addition to changes in the immediate vicinity of the binding site, small molecule-wide structural adjustments accommodate ligand binding. Our studies show that unstructured peptides, such as the BH3 domains, behave like their structured counterparts and can bind tightly and selectively in an enthalpically driven process.

Selected figure(s)

Figure 3.
Fig. 3. Comparison of backbone conformations of Mcl-1:Puma with other Bcl-2 proteins. The backbone ribbon of Mcl-1:Puma (PDB code 2ROC) is shown in gray in all panels, and the orientation of the Mcl-1 is the same as that in Fig. 2b. (a) Unliganded Mcl-1 (PDB code 1WSX^15) in gold. The positions of H205 and H233 are shown. (b) Bcl-x[L]:Bim (PDB code 1PQ1^9) in pink (BH3 ligands not shown). (c) A1:Puma (PDB code 2VOF^19) in green. (d) Unliganded Bcl-x[L] (PDB code 1PQ0^9) in blue.

Figure 5.
Fig. 5. BH3 domains are unstructured in solution. (a) Detail of NoxaB binding Mcl-1 (PDB code 2NL9^10) showing the NWGR motif of the BH1 domain α5 and the N-capping interaction. The side chain of N260 forms a hydrogen bond with R263 HN, and an intermolecular N-cap occurs between the side chains of N70 and G262. The BH3 helix is coloured yellow, and the key side chains are illustrated. (b) CD spectra of the BH3 domains for Puma (orange), NoxaA (blue), NoxaB (red) and Bim (green) are shown in the presence (square/line) and in the absence (line only) of 30% trifluoroethanol.

The above figures are reprinted by permission from Elsevier: J Mol Biol (2008, 380, 958-971) copyright 2008.

Figures were selected by the author.